Package index • chromatographR

Package overview

chromatographR chromatographR-package: chromatographR: Chromatographic Data Analysis Toolset

reexports read_chroms: Read chromatograms.
preprocess(): Preprocess time/wavelength data
subtract_blanks(): Subtract blank chromatograms
correct_rt(): Retention time alignment via time warping
correct_rt_group(): Correct retention time with group-based warping
correct_peaks(): Correct peak positions according to a PTW warping model
get_peaks(): Get peak list
get_peaktable(): Convert peak lists into an aligned peak table
get_spectra(): Extract a spectrum from a chromatogram
attach_metadata(): Attaches sample metadata to a peak_table object by matching sample names.
attach_ref_spectra(): Attach reference spectra to a peak_table object.
normalize_data(): Normalize peak table or chromatograms
cluster_spectra(): Cluster spectra

plot_all_spectra(): Plot all spectra for chosen peak
plot_chroms(): Plot traces from list of chromatograms
plot_chroms_heatmap(): Plot chromatograms as heatmap
plot_spectrum(): Plot spectrum from peak table
plot_spectrum_inset(): Plot a chromatogram or chromatograms with an inset UV spectrum
annotate_peaks(): Annotate peaks on a chromatogram
boxplot(<peak_table>): Make boxplot from peak table.
mirror_plot(): Make mirror plot from peak table
scan_chrom(): Plot spectra by clicking on the chromatogram
plot(<peak_list>): Overlay fitted peak shapes on chromatograms
plot(<peak_table>): Plot spectrum from peak table
plot(<ptw_list>): Plot PTW alignments

print(<peak_table>): Print peak table
print(<peak_list>): Print peak list
summary(<peak_table>): Summarize Peak Table
`[`(<peak_table>): Subset peak table
`[`(<peak_list>): Subset peak list
dim(<peak_table>): Return dimensions of a peak_table object.
head(<peak_table>) tail(<peak_table>): Return first or last parts of a peak_table.
row.names(<peak_table>): Return row names from a peak_table object.
subset(<peak_table>): Subset peak table